tabdev {labdsv} | R Documentation |
Calculates the species (column-wise) and total deviance of a classified vegetation data frame
veg,clustering,nitr=1000)
veg |
a vegetation (or other taxon) data frame |
clustering |
an integer vector specifying class membership for each plot |
Calculates the relative abundance of taxa in classes, and then calculates the deviance associated with that taxon. Total table deviance is simple the sum of species deviances. It calculates the probability of obtaining as low a deviance as observed by permuting the species values nitr-1 times. the p-val is then calculated as (n+1)/nitr where n is the number of cases with values as low or lower than observed.
a list wit components:
spcdev |
a dataframe with columns species, deviance, p-value |
totdev |
total table deviance |
Table deviance is a useful way to test the validity of clusters derived by other means, including cutting hierarchical cluster analyses of non-hierarchical approaches. In addition, it is useful for identifying species of interest in the local flora.
David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/labdsv
http://ecology.montana.msu.edu/labdsv
data(bryceveg) # retrieves a vegetation data frame clust <- sample(1:5,nrow(bryceveg),replace=TRUE) tabdev(bryceveg,clust)